152
T. A. Zubatiuk et al.
only positive eigenvalues. The energy of zero point vibrations was calculated at the
same level of theory (B3LYP/aug-cc-pvdz) within the harmonic approximation. Influence of environment on relative stability of conformers was estimated by single
point calculations using Polarized Continuum Model (PCM) [57–59] and water as
a solvent at the same level of theory.
The results of calculations demonstrate that the set of stable conformers of methyl esters of DNTs corresponds well to the structures considered in the previous
studies [19, 20, 52]. The revealed species include south/anti and north/anti conformers of all molecules (Fig. 5.10), south/syn and north/syn conformers of mGMP
(Fig. 5.11), and north/syn conformers of mCMP and mAMP with orthogonal orientation of base with respect to ribose (Fig. 5.12). But in addition to our previous
investigations, south/syn conformer of mAMP was also found. Existence of this
rare conformer is possible because presence of intramolecular C–H…N hydrogen
bond. This conformer corresponds to minimum on energy surface which is nearest
to syn-conformer of mAMP in ZI–ZII–DNA form. Such a distribution of minima on
the PES of the molecule of methyl nucleotide repeats and confirms the results of the
conformational analysis performed for DNTs anions with P–OH fragment.
An absence of “artificial” intramolecular hydrogen bonds results in a change of
relative stability of anti-conformers of mGMP. Unlike previous studies, here the
south/anti conformer of mGMP is more stable than the north/anti form. However,
the syn conformers of this nucleotide are considerably more stable (Table 5.6) due
to the formation of intramolecular N–H…O hydrogen bond, in agreement with the
previous findings [19, 20, 52].
Fig. 5.11 The structure of S/
syn and N/syn conformers of
mGМР
Fig. 5.10 The structure of S/
anti and N/anti conformers
of anions of 2′-deoxyribonucleotides. mTMP molecule
is shown as representative
example
Fig. 5.12 The structure of
north/syn conformers of
mCMP and mAMP with
orthogonal orientation of base
with respect to ribose
T. A. Zubatiuk et al.
only positive eigenvalues. The energy of zero point vibrations was calculated at the
same level of theory (B3LYP/aug-cc-pvdz) within the harmonic approximation. Influence of environment on relative stability of conformers was estimated by single
point calculations using Polarized Continuum Model (PCM) [57–59] and water as
a solvent at the same level of theory.
The results of calculations demonstrate that the set of stable conformers of methyl esters of DNTs corresponds well to the structures considered in the previous
studies [19, 20, 52]. The revealed species include south/anti and north/anti conformers of all molecules (Fig. 5.10), south/syn and north/syn conformers of mGMP
(Fig. 5.11), and north/syn conformers of mCMP and mAMP with orthogonal orientation of base with respect to ribose (Fig. 5.12). But in addition to our previous
investigations, south/syn conformer of mAMP was also found. Existence of this
rare conformer is possible because presence of intramolecular C–H…N hydrogen
bond. This conformer corresponds to minimum on energy surface which is nearest
to syn-conformer of mAMP in ZI–ZII–DNA form. Such a distribution of minima on
the PES of the molecule of methyl nucleotide repeats and confirms the results of the
conformational analysis performed for DNTs anions with P–OH fragment.
An absence of “artificial” intramolecular hydrogen bonds results in a change of
relative stability of anti-conformers of mGMP. Unlike previous studies, here the
south/anti conformer of mGMP is more stable than the north/anti form. However,
the syn conformers of this nucleotide are considerably more stable (Table 5.6) due
to the formation of intramolecular N–H…O hydrogen bond, in agreement with the
previous findings [19, 20, 52].
Fig. 5.11 The structure of S/
syn and N/syn conformers of
mGМР
Fig. 5.10 The structure of S/
anti and N/anti conformers
of anions of 2′-deoxyribonucleotides. mTMP molecule
is shown as representative
example
Fig. 5.12 The structure of
north/syn conformers of
mCMP and mAMP with
orthogonal orientation of base
with respect to ribose